Curator Dashboard

An algorithm that generates lists of genes associated with a gene or one or more disorders. The algorithm can be used in high-throughput screening experiments, can create disease-specific micro-arrays, and can sort the results of gene profiling data. Based on the co-citations of all Medline records, MedGene can retrieve the following relationships: 1. A list of human genes associated with a particular human disease in ranking order 2. A list of human genes associated with multiple human diseases in ranking order 3. A list of human diseases associated with a particular human gene in ranking order 4. A list of human genes associated with a particular human gene in ranking order 5. The sorted gene list from other disease related high-throughput experiments, such as micro-array 6. The sorted gene list from other gene related high-throughput experiments, such as micro-array

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• SciCrunch
• 17 years ago - by Anonymous

This database currently holds E-MAP scores (individual interactions and correlation coefficients) for budding yeast genes involved in the early secretory pathway and chromosome function (including DNA damage and repair, transcriptional control, chromosome segregation and telomere regulation). E-MAPs (Epistatic Mini Array Profiles) are formed by creating and quantifying high-density genetic interaction maps. With this method, observed double mutant colony sizes are compared to those that would be expected from a distribution of typical double mutant colonies of each strain. Each interaction is assigned a score, which indicates the magnitude of the difference from the expected value and the certainty of the score. Negative (or aggravating) scores (< -2.5) correspond to synthetic sick/lethal interactions while positive (or alleviating) scores (> +2.5) corresponds to epistatic or suppressor interactions.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. LINNEA Pathways is a user-friendly comprehensive online resource for gene- or protein-based scientific research. It is based on a total of 248 signaling and metabolic human biological pathway maps created for Invitrogen by GeneGo. The current version of iPath features 225 maps displaying human regulatory and metabolic pathways established in experimental literature produced by MetaCore from GeneGo, Inc. The map objects (proteins, genes, EC functions, and compounds) are connected via metabolic transformations and physical protein interactions, which were assembled by the GeneGo team of experienced annotators, geneticists, and biochemists. The pathways are organized in a vertical fashion following the general signaling path from signaling molecules and membrane receptors, via signal transduction cascades, to transcription factors and their gene targets. Following the natural organization of cellular machinery with highly interconnected pathways and modules, many maps are linked together via hyperlinked box symbols. Such linkage allows the reconstruction of a big picture view of human cell biology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

ITFP is an integrated transcription factor (TF) platform, which included abundant TFs and targets message of mammalian. Support vector machine (SVM) algorithm combined with error-correcting output coding (ECOC) algorithm was utilized to identify and classify transcription factor from protein sequence of Human, Mouse and Rat. For transcription factor targets, a reverse engineering method named ARACNE was used to derive potential interaction pairs between transcription factor and downstream regulated gene from Human, Mouse and Rat gene expression profile data. Detailed information of gene expression profile data can be found in help page. Moreover, all data provided by the platform is free for non-commercial users and can be downloaded through links on help page.

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• SciCrunch
• 17 years ago - by Anonymous

iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from nine different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. Integration is achieved through a rigorously documented procedure for mapping protein IDs across databases, enabling systematic backtracking of the links used to establish the identity of the interaction partners. The iRefWeb interface groups interaction records from the different databases into a single non-redundant view. In particular iRefWeb facilitates comparing interaction records as seen by the various source databases relative to the PubMeds they were annotated from. iRefWeb is one of several views of the iRefIndex resource. Data are also available in a tab-delimited plain-text format (PSI-MITAB) as well as planned releases of a PSI-XML formatted version and a Cytoscape plugin. Further details about the iRefIndex project as well as data downloads are available from here . The method used to build iRefIndex is described in a recent publication.

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• SciCrunch
• 17 years ago - by Anonymous

A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base .

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• SciCrunch
• 17 years ago - by Anonymous

The Human Cancer Pathway Protein Interaction Network (HCPIN) was constructed as a step toward better integrating protein three-dimensional (3D) structural information in cancer systems biology. It was constructed by analysis of several classical cancer-associated signaling pathways and their physical protein-protein interactions. The HCPIN Website provides a comprehensive description of this biomedically important multipathway network together with experimental and homology models of HCPIN proteins useful for cancer biology research.

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• SciCrunch
• 17 years ago - by Anonymous

A database for facilitating the analysis of Drug Binding Competitiveness. It contains information about Computed Ligand-Receptor Interaction Energy and other attributes such as energy components; ligand classification, functions and properties. Ligand structure is also included. The database now contains 67,184 entries, in which there are 5,978 distinctive ligands and 2,258 distinctive receptors.

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• SciCrunch
• 17 years ago - by Anonymous

Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource.

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• SciCrunch
• 17 years ago - by Anonymous

Public healthcare network in Sherbrooke, Quebec, Canada, affiliated with the Université de Sherbrooke Faculty of Medecine.

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• SciCrunch
• 13 years ago - submitted by Andrea Stagg

A database of biochemical pathways that provides access to metabolic transformations and cellular regulations derived from the Roche Applied Science Biochemical Pathways wall chart.

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• SciCrunch
• 17 years ago - by Anonymous

Athena is a web-based application that warehouses disparate datatypes related to the control of gene expression. Athena provides several features to enable exploration of the regulatory mechanisms of Arabidopsis gene control. The first main tool we provide is visualization of promoter domains of selected genes. Database crossreference for these transcription factors is provided as well as a statistical test for enrichment of binding activity within the set of selected promoters. The data mining tools in Athena allow for selection of sets of genes based on two different factors. -Genes can be select by specifying a set of binding factors whose putative sites must be present within all of those genes'' promoter regions. -Alternatively, genes can be selected using Gene Ontology annotations. Both GO (Gene Ontology) Slim terms and Gene Ontology terms are available. One can select a set of genes by either choosing a union of the genes annotated by a selected set of Slim terms or Gene Ontology terms. The selected gene''s putative binding factors are listed, including enrichment data. Furthermore, enriched presence of Gene Ontology terms is given. The analysis suite provides both enhanced data mining tools for selecting genes as well as several data displays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

Curated species-specific database present at the Plant Metabolic Network. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

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• SciCrunch
• 16 years ago - by Anonymous

Software application that map QTLs in F-2 intercross in model organisms (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Doodle is a database that was developed to store and distribute information about the protein oligomerization domains that are encoded by various genomes. The protein oligomerization domains described here were found using the lambda repressor fusion system. Doodle uses a schema that is based on EnsEMBL, while also utilizing bioperl modules to both store and retrieve data. The frontend was developed entirely in perl, while the backend utilizes MySQL. GMOD was used to develop the genomic view.

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• SciCrunch
• 17 years ago - by Anonymous

Version 1.0 database for neuro-endocrine-immune (dbNEI) is a web-based knowledge resource specific for the NEI systems. It provides a knowledge environment for understanding the main regulatory systems of NEI in a molecular level. dbNEI provides a knowledge environment for understanding the main regulatory systems of NEI in a molecular level. dbNEI collects 1,058 NEI related signal molecules, their 940 interactions and 72 affiliated tissues from the Cell Signaling Networks database and manually selects 982 NEI papers from PubMed. NEI related information, such as signal transductions, regulations and control subunits, are integrated. Especially, dbNEI represents as graphic visualization, by which control subunits can be automatically obtained according to the inquiring issues. Version 2.0: We updated the database in four aspects. 1. Recruiting new NEI genes and compounds. 2. Adding KEGG,HPRD,Transcription factor and microRNA target relations. 3. Collecting drug-gene and disease-gene relation. 4. Building multi-layer network for drug-NEI-disease.

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• SciCrunch
• 17 years ago - by Anonymous

A database of imaging probes useful for preclinical and clinical studies. The National Institute of Mental Health (NIMH) and the Society for Non-Invasive Imaging in Drug Development (SNIDD) are in the process of creating a centralized, searchable PET, SPECT, and MRI tracer database as a resource for the scientific community. The goal of this effort is to promote the use of imaging probes in preclinical and clinical research and in drug discovery to accelerate the identification and validation of novel targets for therapeutic intervention in human diseases, especially those with central nervous system components. NIMH will maintain the tracer database as part of the Psychoactive Drug Screening Program (PDSP). The database will contain records for each radiotracer with relevant information such as target, research uses, pharmacology, pharmacokinetics, synthesis protocols, toxicology and safety data, dosimetry, other clinical data, IND info, permission to cross-reference pharmacology, toxicology, or safety data in a drug master file (if an IND exists), contact information, patent, etc. with appropriate safeguards in place to protect the intellectual property of proprietary compounds.

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• SciCrunch
• 17 years ago - by Anonymous

A statistical method for interpreting variations in protein sequence (e.g. coding SNPs in the population, SNVs in cancer genomes) in the context of protein post-translational signaling modifications.

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• SciCrunch
• 13 years ago - by Anonymous

Minimaps are designed to supplement the Metabolic Pathways Charts by enlarging selected major individual pathways so as to illustrate additional aspects of metabolism such as Membranes, Compartmentation, Organs, Organelles, Shuttles and Regulation. The selection is designed to stimulate the exploration of the pathways and make metabolism more meaningful.

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• SciCrunch
• 17 years ago - by Anonymous

An organization that is centered around the education of younger Parkinson's disease patients as well as their families, friends and healthcare professionals. They primarily provide educational and support programs and services that are designed to help younger Parkinson's patients manage the disease and maintain a healthy lifestyle. The center provides information about treatment options, clinical trials, support groups, person to person chats, local chapters,regional referral information, and Parkinson's related events.

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• SciCrunch
• 17 years ago - by Anonymous